J
Jason O'Rawe
Researcher at Cold Spring Harbor Laboratory
Publications - 25
Citations - 1258
Jason O'Rawe is an academic researcher from Cold Spring Harbor Laboratory. The author has contributed to research in topics: Indel & Exome sequencing. The author has an hindex of 10, co-authored 25 publications receiving 1124 citations. Previous affiliations of Jason O'Rawe include Stony Brook University.
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Journal ArticleDOI
Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing
Jason O'Rawe,Jason O'Rawe,Tao Jiang,Guangqing Sun,Yiyang Wu,Yiyang Wu,Wei Min Wang,Jingchu Hu,Paul Bodily,Lifeng Tian,Hakon Hakonarson,W. Evan Johnson,Zhi Wei,Kai Wang,Kai Wang,Gholson J. Lyon,Gholson J. Lyon,Gholson J. Lyon +17 more
TL;DR: The results suggest that more caution should be exercised in genomic medicine settings when analyzing individual genomes, including interpreting positive and negative findings with scrutiny, especially for indels.
Journal ArticleDOI
Accurate de novo and transmitted indel detection in exome-capture data using microassembly
Giuseppe Narzisi,Jason O'Rawe,Ivan Iossifov,Han Fang,Yoon-ha Lee,Zihua Wang,Yiyang Wu,Gholson J. Lyon,Michael Wigler,Michael C. Schatz +9 more
TL;DR: Scalpel's power to detect long (≥30 bp) transmitted events and enrichment for de novo likely gene-disrupting indels in autistic children and a detailed repeat analysis coupled with a self-tuning k-mer strategy allows Scalpel to outperform other state-of-the-art approaches for indel discovery.
Journal ArticleDOI
Reducing INDEL calling errors in whole genome and exome sequencing data
Han Fang,Yiyang Wu,Giuseppe Narzisi,Jason O'Rawe,Jason O'Rawe,Laura T Jimenez Barron,Julie Rosenbaum,Michael Ronemus,Ivan Iossifov,Michael C. Schatz,Gholson J. Lyon,Gholson J. Lyon +11 more
TL;DR: This work characterized whole genome sequencing, whole exome sequencing, and PCR-free sequencing data from the same samples to investigate the sources of INDEL errors and developed a classification scheme based on the coverage and composition to rank high and low quality INDEL calls.
Journal ArticleDOI
Indel variant analysis of short-read sequencing data with Scalpel
Han Fang,Han Fang,Ewa A. Bergmann,Kanika Arora,Vladimir Vacic,Michael C. Zody,Ivan Iossifov,Jason O'Rawe,Jason O'Rawe,Yiyang Wu,Yiyang Wu,Laura T Jimenez Barron,Laura T Jimenez Barron,Julie Rosenbaum,Michael Ronemus,Yoon-ha Lee,Zihua Wang,Esra Dikoglu,Vaidehi Jobanputra,Gholson J. Lyon,Gholson J. Lyon,Michael Wigler,Michael C. Schatz,Michael C. Schatz,Giuseppe Narzisi +24 more
TL;DR: This protocol describes how to use Scalpel to perform highly accurate indel calling from whole-genome and whole-exome sequencing data and provides detailed instructions for an exemplary family-based de novo study.
Journal ArticleDOI
TAF1 Variants Are Associated with Dysmorphic Features, Intellectual Disability, and Neurological Manifestations.
Jason O'Rawe,Jason O'Rawe,Yiyang Wu,Yiyang Wu,Max Dorfel,Alan F. Rope,P.Y. Billie Au,Jillian S. Parboosingh,Sungjin Moon,Maria Kousi,Konstantina Kosma,Konstantina Kosma,Christopher Smith,Maria Tzetis,Maria Tzetis,Jane L. Schuette,Robert B. Hufnagel,Robert B. Hufnagel,Carlos E. Prada,Francisco Martínez,Carmen Orellana,Jonathan Crain,Alfonso Caro-Llopis,Silvestre Oltra,Sandra Monfort,Laura T. Jiménez-Barrón,Laura T. Jiménez-Barrón,Jeffrey Swensen,Sara Ellingwood,Rosemarie Smith,Han Fang,Sandra Ospina,Sander Stegmann,Nicolette S. den Hollander,David Mittelman,Gareth Highnam,Reid J. Robison,Edward Yang,Laurence Faivre,Agathe Roubertie,Jean Baptiste Rivière,Kristin G. Monaghan,Kai Wang,Erica E. Davis,Nicholas Katsanis,Vera M. Kalscheuer,Edith H. Wang,Kay Metcalfe,Tjitske Kleefstra,A. Micheil Innes,Sophia Kitsiou-Tzeli,Mónica Roselló,Catherine E. Keegan,Gholson J. Lyon,Gholson J. Lyon,Gholson J. Lyon +55 more
TL;DR: It is suggested that mutations in TAF1 play a critical role in the development of this X-linked ID syndrome, and knockdown and mutant studies of this gene in zebrafish have shown a quantifiable effect on a neuronal phenotype.